"A subpoena has been issued to Michael Cohen for relevant information in light of the public disclosures made yesterday," James Gazzale, a spokesperson for the New York State Department of Taxation and Finance, told CNBC on Wednesday.
A source familiar with the investigation told CNBC that anything the Tax Department uncovers through its investigation will be referred to the New York State Attorney General's Office for prosecution.
Cohen pleaded guilty on Tuesday to eight criminal charges, including tax fraud and campaign finance crimes, in New York federal court.
He said that during the 2016 presidential campaign he had unlawfully facilitated payments to two women who have said they had sex with the president. Trump and his lawyers have denied wrongdoing.
Gazzale said his department will work with the Attorney General's office, as well as the Manhattan District Attorney.
Cohen's lawyer, former Clinton White House aide Lanny Davis, has said Trump himself "directed" Cohen "to commit a crime."
Davis has also expressed a willingness for Cohen to cooperate with state and federal prosecutors, including special counsel Robert Mueller, who is investigating Russian meddling in the 2016 presidential election.
New York's Attorney General Barbara Underwood had filed suit against Trump and members of his family in June, alleging a pattern of "persistently illegal conduct" at the nonprofit foundation.
Underwood accused the nonprofit of engaging in "extensive unlawful political coordination with the Trump presidential campaign," according to the suit.
Trump responded furiously on Twitter, vowing not to settle the case.
"As our lawsuit against the Trump Foundation illustrates, we will hold Donald Trump and his associates accountable for violations of state law, and will seek a criminal referral from the appropriate state agency as necessary," a spokeswoman for the Attorney General's office told CNBC.
A spokesman for the Southern District of New York's federal court denied any knowledge of the subpoena.
Cohen had served as Trump's legal counsel and a leader at the Trump Organization, as well as deputy finance chairman of the Republican National Committee.
He came under fire after The Wall Street Journal reported that he made a $130,000 payment to adult-film star Stormy Daniels as part of a nondisclosure agreement she signed before the 2016 election.
Daniels is suing Trump and Cohen to void that contract, which bars her from discussing an alleged affair with Trump from years earlier. The White House has denied the affair.
This story is developing. Please check back for updates.
--CNBC's Dan Mangan contributed to this report.